The search for reliable biomarkers sits at the heart of modern drug development and precision medicine. From predicting therapeutic response to stratifying patient populations, biomarkers are essential for translating molecular insights into clinical decision-making. For years, researchers have relied heavily on genomic and transcriptomic analyses to identify new biomarker candidates. Proteomics has followed as technologies have matured.
Yet one crucial layer of biology has remained largely inaccessible in the most common tissue format used in both research and clinical settings: metabolomics in formalin-fixed paraffin-embedded (FFPE) samples. This changes with the introduction of Panome Bio’s TissueBridge™ FFPE Metabolomics services.
Why Metabolites Matter in Biomarker Discovery
While DNA and RNA provide information about genetic predispositions and transcriptional activity, metabolites reflect the real-time phenotype of tissues. They capture dynamic biological processes such as cellular energy states, signaling pathways, nutrient availability, and the biochemical effects of drugs. This makes them uniquely powerful for biomarker discovery. Metabolites provide mechanistic insights into how disease alters cellular pathways, they reveal treatment response signatures that may not be apparent at the genetic or transcript level, and they connect biology with external influences such as diet, the microbiome, or environmental exposures.
By complementing genomics, transcriptomics, and proteomics, metabolomics contributes to a more complete molecular profile of the patient: one that is both mechanistically rich and clinically actionable.
The Untapped Potential of FFPE Samples for Metabolic Insights
Most clinically valuable tissues are stored as FFPE blocks. These include biopsies from pivotal clinical trials, surgical resections from oncology patients with years of follow-up data, and rare disease samples archived at specialty centers. FFPE represents the largest and most clinically annotated archive of patient tissue in the world. But until recently, extracting high-quality metabolomic information from these samples was not feasible.
Now, with Panome Bio’s advances in sample preparation and data analysis methods, it is possible to generate reproducible metabolic profiles directly from FFPE tissues. TissueBridge™ FFPE Metabolomics. enables biomarker researchers to tap into a vast resource that has been largely inaccessible for metabolomics in the past.
Applications in Translational Research
TissueBridgeFFPE Metabolomics opens up high-value opportunities across a range of research areas. In oncology, researchers can identify metabolic signatures associated with tumor progression, therapy resistance, or response to immunotherapies, and they can revisit archived tumor blocks from completed clinical trials to uncover predictive markers that were previously overlooked. In drug response studies, archived samples from earlier-phase trials can be used to better understand why some patients responded to therapy while others did not, and to uncover metabolic shifts induced by drug candidates that help clarify mechanisms of action. Rare and difficult-to-access cohorts can also be studied, since many rare disease samples exist only in FFPE archives. For these patients, metabolomics makes it possible to generate new insights without the need for fresh collections.
Perhaps most powerfully, through Panome Bio’s integrated multi-omics analysis, metabolomics can be integrated with genomic, transcriptomic, and proteomic data already obtained from the same FFPE blocks. This creates the opportunity to build multi-dimensional biomarker signatures that offer stronger predictive power than any single “omic” layer alone.
Retrospective Power: Linking to Clinical Outcomes
One of the most exciting opportunities lies in retrospective research. Many archived FFPE samples are tied to long-term clinical records, including survival outcomes, recurrence data, and detailed treatment histories. By generating metabolic profiles from these tissues, researchers can directly connect molecular patterns to clinical outcomes. This ability transforms biobanks from passive archives into active discovery platforms, providing a powerful way to accelerate translational research without the cost and delay of recruiting new patient cohorts or launching new trials.
Conclusion
TissueBridge FFPE Metabolomics represents a major step forward for biomarker discovery and translational science. For the first time, researchers will be able to integrate metabolic information with genomic and proteomic data from the world’s most abundant and clinically annotated tissue format. The result is a new ability to discover biomarkers that reflect real-time biology, re-examine archived cohorts for fresh insights, and advance drug development and precision medicine by leveraging resources that are already available.
At Panome Bio, we are proud to enable TissueBridge FFPE Metabolomics – the capability of Next-Generation Metabolomics to analyze FFPE tissue samples – and look forward to collaborating with partners who want to expand the frontiers of biomarker discovery.
Learn more about TissueBridge metabolomicsRead the full data reportLearn more about FFPE